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firepony's Introduction

Firepony

Firepony is a C++/CUDA reimplementation of the GATK base quality score recalibration algorithm.

It is meant to act as a fast drop-in replacement for GATK BQSR in sequence analysis pipelines. The output of Firepony can be consumed by GATK for subsequent processing steps.

Firepony can run on both x86 CPUs and NVIDIA GPUs. Because it was designed from the ground-up in a data-parallel fashion, Firepony scales extremely well across both architectures.

https://github.com/broadinstitute/firepony/wiki

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firepony's Issues

Lift module

Could you please explain the 'life' module ? Thanks.

cmake ..
-- The C compiler identification is PGI 22.7.0
-- The CXX compiler identification is PGI 22.7.0
-- Check for working C compiler: /opt/nvidia/hpc_sdk/Linux_x86_64/22.7/compilers/bin/nvc
-- Check for working C compiler: /opt/nvidia/hpc_sdk/Linux_x86_64/22.7/compilers/bin/nvc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /opt/nvidia/hpc_sdk/Linux_x86_64/22.7/compilers/bin/nvc++
-- Check for working CXX compiler: /opt/nvidia/hpc_sdk/Linux_x86_64/22.7/compilers/bin/nvc++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done

CMake Error at CMakeLists.txt:17 (add_subdirectory):
  The source directory

    /path/to/firepony/modules/lift

  does not contain a CMakeLists.txt file.

Firepony segmentation fault

For this command and input files of ~30KB I got Segmentation fault:

firepony --cpu-only -r samples/example_human_reference.fasta -dv -s samples/example_human_known_snp.vcf samples/example_human_Illumina.realigned.bam
Firepony v1.1.0
enabled compute devices:
CPU (Intel Threading Building Blocks, 7 threads)

original command line: --cpu-only -r samples/example_human_reference.fasta -dv -s samples/example_human_known_snp.vcf samples/example_human_Illumina.realigned.bam
computed command line: -r samples/example_human_reference.fasta -s samples/example_human_known_snp.vcf -o - --batch-size 1000 --debug --cpu-only --verbose

loaded index for samples/example_human_reference.fasta
loading variant database samples/example_human_known_snp.vcf...[W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'RSPOS' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'dbSNPBuildID' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'SSR' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'SAO' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'VP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'GENEINFO' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'WGT' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'VC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'INT' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'ASP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'VLD' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'GNO' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'OTHERKG' is not defined in the header, assuming Type=String
Segmentation fault (core dumped)

Any ideas what went wrong?

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